How to use Blender in a way that allows easy modifications
Try the same thing again. However this time don't apply the boolean modifier on your original object set, just keep them active. You can take your original objects by duplication and hide them on a different layer. This way if you need to make a modification, you can duplicate them back to your working layer, make the desired changes, and on the working layer only apply the modifier(s).

So that you have a bit more visual context to what this means, here is the break-down:

Here are the ways that I split up the layers:

Layer 1 (Homerow 1) = The Active Layer

Layer 2 (Homerow 2) = The Stored Object Being Subtracted From

Layer 11 (Shift + Homerow 1) = The Stored Object Being Subtracted.

Here are the screen shots in the order listed:







Here is the modification workflow after you find the need to change something: